Tree Genetics & Genomes最新文献

{"title":"Genome-wide SNP discovery in native American and Hungarian Robinia pseudoacacia genotypes using next-generation double-digest restriction-site-associated DNA sequencing (ddRAD-Seq)","authors":"Z. Köbölkuti, E. Tóth, Z. Keserű, J. Fike, Bence Bolla, T. Ábri, A. Borovics, A. Benke, Klára Cseke","doi":"10.1007/s11295-023-01589-8","DOIUrl":"https://doi.org/10.1007/s11295-023-01589-8","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43280418","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide association analysis and validation with KASP markers for nut and shell traits in almond (Prunus dulcis [Mill.] D.A.Webb)","authors":"Gina M. Sideli, D. Mather, M. Wirthensohn, F. Dicenta, Shashi N. Goonetilleke, P. Martínez-García, T. Gradziel","doi":"10.1007/s11295-023-01588-9","DOIUrl":"https://doi.org/10.1007/s11295-023-01588-9","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44512540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parametric mapping of QTL for resistance to European canker in apple in ‘Aroma’ × ‘Discovery’","authors":"J. Skytte af Sätra, F. Odilbekov, P. Ingvarsson, E. van de Weg, L. Garkava-Gustavsson","doi":"10.1007/s11295-023-01587-w","DOIUrl":"https://doi.org/10.1007/s11295-023-01587-w","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45370807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"On the accuracy of threshold genomic prediction models for leaf miner and leaf rust resistance in arabica coffee","authors":"H. F. Carvalho, L. F. V. Ferrão, Giovanni Galli, J. Nonato, L. Padilha, M. Maluf, Márcio Fernando Ribeiro de Resende, R. Fritsche‐Neto, O. Guerreiro-Filho","doi":"10.1007/s11295-022-01581-8","DOIUrl":"https://doi.org/10.1007/s11295-022-01581-8","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41985419","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification, expression analysis, and functional verification of the JMJ (Jumonji) histone demethylase gene family in pear (Pyrus bretchneideri)","authors":"Waqar Khan, Weijuan Liu, Zhe Liu, Xiaoxuan Zhu, Juyou Wu, Peng Wang","doi":"10.1007/s11295-023-01586-x","DOIUrl":"https://doi.org/10.1007/s11295-023-01586-x","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47044224","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and structure of seed pools in an old planted Pinus thunbergii population and seed collection strategy for gene preservation","authors":"Masakazu G. Iwaizumi, Aziz Akbar Mukasyaf, I. Tamaki, J. Nasu, N. Miyamoto, M. Tamura, A. Watanabe","doi":"10.1007/s11295-022-01584-5","DOIUrl":"https://doi.org/10.1007/s11295-022-01584-5","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47683712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genomic prediction in a multi-generation Eucalyptus globulus breeding population","authors":"Geoffrey Haristoy, L. Bouffier, Luis Fontes, Luis Leal, J. Paiva, J. Pina, J. Gion","doi":"10.1007/s11295-022-01579-2","DOIUrl":"https://doi.org/10.1007/s11295-022-01579-2","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43976495","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Making headway toward enduring changes: perspectives on breeding tree crops through genome editing","authors":"R. T. Pinto, Chanaka Roshan Abeyratne, L. V. Paiva, V. Benedito","doi":"10.1007/s11295-022-01583-6","DOIUrl":"https://doi.org/10.1007/s11295-022-01583-6","url":null,"abstract":"","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43063260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A novel synthesis of two decades of microsatellite studies on European beech reveals decreasing genetic diversity from glacial refugia.","authors":"Camilla Stefanini, Katalin Csilléry, Bartosz Ulaszewski, Jarosław Burczyk, Michael E Schaepman, Meredith C Schuman","doi":"10.1007/s11295-022-01577-4","DOIUrl":"10.1007/s11295-022-01577-4","url":null,"abstract":"<p><p>Genetic diversity influences the evolutionary potential of forest trees under changing environmental conditions, thus indirectly the ecosystem services that forests provide. European beech (<i>Fagus sylvatica</i> L.) is a dominant European forest tree species that increasingly suffers from climate change-related die-back. Here, we conducted a systematic literature review of neutral genetic diversity in European beech and created a meta-data set of expected heterozygosity (<i>He</i>) from all past studies providing nuclear microsatellite data. We propose a novel approach, based on population genetic theory and a min-max scaling to make past studies comparable. Using a new microsatellite data set with unprecedented geographic coverage and various re-sampling schemes to mimic common sampling biases, we show the potential and limitations of the scaling approach. The scaled meta-dataset reveals the expected trend of decreasing genetic diversity from glacial refugia across the species range and also supports the hypothesis that different lineages met and admixed north of the European mountain ranges. As a result, we present a map of genetic diversity across the range of European beech which could help to identify seed source populations harboring greater diversity and guide sampling strategies for future genome-wide and functional investigations of genetic variation. Our approach illustrates how to combine information from several nuclear microsatellite data sets to describe patterns of genetic diversity extending beyond the geographic scale or mean number of loci used in each individual study, and thus is a proof-of-concept for synthesizing knowledge from existing studies also in other species.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11295-022-01577-4.</p>","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":2.4,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9744708/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10595585","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Additive and non-additive genetic variance in juvenile Sitka spruce (<i>Picea sitchensis</i> Bong. Carr).","authors":"J J Ilska, D J Tolhurst, H Tumas, J P Maclean, J Cottrell, S J Lee, J Mackay, J A Woolliams","doi":"10.1007/s11295-023-01627-5","DOIUrl":"10.1007/s11295-023-01627-5","url":null,"abstract":"<p><p>Many quantitative genetic models assume that all genetic variation is additive because of a lack of data with sufficient structure and quality to determine the relative contribution of additive and non-additive variation. Here the fractions of additive (<i>f</i>_<i>a</i>) and non-additive (<i>f</i>_<i>d</i>) genetic variation were estimated in Sitka spruce for height, bud burst and pilodyn penetration depth. Approximately 1500 offspring were produced in each of three sib families and clonally replicated across three geographically diverse sites. Genotypes from 1525 offspring from all three families were obtained by RADseq, followed by imputation using 1630 loci segregating in all families and mapped using the newly developed linkage map of Sitka spruce. The analyses employed a new approach for estimating <i>f</i>_<i>a</i> and <i>f</i>_<i>d</i>, which combined all available genotypic and phenotypic data with spatial modelling for each trait and site. The consensus estimate for <i>f</i>_<i>a</i> increased with age for height from 0.58 at 2 years to 0.75 at 11 years, with only small overlap in 95% support intervals (<i>I</i>₉₅). The estimated <i>f</i>_<i>a</i> for bud burst was 0.83 (<i>I</i>₉₅=[0.78, 0.90]) and 0.84 (<i>I</i>₉₅=[0.77, 0.92]) for pilodyn depth. Overall, there was no evidence of family heterogeneity for height or bud burst, or site heterogeneity for pilodyn depth, and no evidence of inbreeding depression associated with genomic homozygosity, expected if dominance variance was the major component of non-additive variance. The results offer no support for the development of sublines for crossing within the species. The models give new opportunities to assess more accurately the scale of non-additive variation.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s11295-023-01627-5.</p>","PeriodicalId":23335,"journal":{"name":"Tree Genetics & Genomes","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10632294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134649859","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}